Everything is wired into the 2 SR29 batteries bank, the SR24 is kept entirely in reserve. So if I drain the 2 SR 29 batteries I move the Battery Switch to combine and use the SR24 to start the boat. I recharge the batteries right after the boat is used with the charger.

Is there any advantage to using the SR24 to always start the boat versus the way it is currently wired?

My guess would be there was a bit or confusion on the explanation. In most setups like yours, 2 SR29's would be only powering your stereo and your 1 SR24 starts your boat and runs all its electronics. I believe when your boat is running, your charging relay is charging your SR24 first and when that reaches a certain voltage, it switches over to your 2 SR29's.

No, with my new setup the accessories, starter, and Stereo are wired into the 2 SR 29's and nothing is drawing from the SR24 unless I combine the batteries via the switch. So the SR24 is a true reserve battery if you will that stays fully charged and unused unless I need it. Everything works just fine but I have wondered if moving the starter to the SR24 has any advantages. Like does it hurt the battery life of the SR24 to not have a regular draw on it.

I'm not real clear on how the ACR manages the charging aspect but my question is more about not drawing off the SR24 unless I combine the batteries via the switch...

With the Blue Sea Add-A-Battery kit you have a unique dual circuit battery switch (with 2 'IN's and 2 'OUT's) and NOT a conventional dual battery switch (with 2 'IN's and a single common 'OUT'). All (100%) of the audio equipment should be wired to the SR29 dual battery bank circuit and the starter & helm buss should be wired to the single SR24 battery. The switch should be normally 'On' when splashed or 'Off' when trailored. You would normally only use the 'Combine' feature if the SR24 starting battery has failed. You can do it differently but the above is the correct way in consideration of the most conditions.
The starting battery does not have to be regularly used in order to promote longevity. On the other hand, using the battery for starting will not measurably shorten its life. It does however, need to see the alternator on a continuous basis and isolated from the other bank when at rest.

If everything is wired to the bank with 2 SRM29's and the SRM24 is strictly a backup battery then it is wired wrong in my opinion. The main boat harness should be running off the SRM24(in normal use) and receive priority charging from the ACR.

If it is running like you are saying then every time you run the stereo while parked and go to start your boat you are starting the boat at low voltage which will seriously shorten the life of your starter and could shorten the life of your alternator, ECM, etc....

^^^^ Brett, a very, very, very good point about regularly starting the boat off the depleted stereo bank after a long stay at rest and allowing the alternator to always see the heaviest load. Defeats the protective aspect of an ACR.